The purpose of this patch is to rename programs with a too generic name, to avoid
conflicts on file names.

--- probcons.orig/Makefile
+++ probcons/Makefile
@@ -35,7 +35,7 @@
 # 3) Dependencies
 ################################################################################
 
-TARGETS = probcons probcons-RNA compare project makegnuplot
+TARGETS = probcons probcons-RNA pc-compare pc-project pc-makegnuplot
 
 .PHONY : all
 all : $(TARGETS)
@@ -43,8 +43,8 @@
 probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc
 	$(CXX) $(CXXFLAGS) -lm -o probcons Main.cc 
 
-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
-	$(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
+pc-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
+	$(CXX) $(CXXFLAGS) -o pc-compare CompareToRef.cc
 
 probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
 	$(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc 
@@ -52,11 +52,11 @@
 fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
 	$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
 
-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
-	$(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc
+pc-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc
+	$(CXX) $(CXXFLAGS) -o pc-project ProjectPairwise.cc
 
-makegnuplot : MakeGnuPlot.cc
-	$(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc
+pc-makegnuplot : MakeGnuPlot.cc
+	$(CXX) $(CXXFLAGS) -o pc-makegnuplot MakeGnuPlot.cc
 
 .PHONY : clean
 clean:
